The explicit-solvent molecular dynamic (MD) simulation and adaptive biased forces (ABF) methods were employed to systemically study the structural and thermodynamic nature of the beta-cyclodextrin (beta CD) monomer, phenanthrene (Phe) monomer, and their inclusion complexes in both the aqueous and membrane environments, aiming at clarifying the atomic-level mechanisms underlying in the CD-enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria. Simulations showed that beta CD and Phe monomers could associate together to construct two distinctive assemblies, i.e, beta CD1-Phe(1) and beta CD2-Phe(1), respectively. The membrane-involved equilibrium simulations and the data of potential of mean forces (PMFs) further confirmed that Phe monomer was capable of penetrating through the membranes without confronting any large energy barrier, whereas, the single beta CD and beta CD-involved assemblies were unable to pass across the membranes. These observations clearly suggested that beta CD only served as the carrier to enhance the bioavailability of Phe rather than the co-substrate in the Phe biodegradation process. The Phe-separation PMF profiles indicated that the maximum of the Phe uptake by bacteria would be achieved by the "optimal" beta CD:Phe molar ratio, which facilitated the maximal formation of beta CD1-Phe(1) inclusion and the minimal construction of beta CD2-Phe(1) complex. (C) 2014 Elsevier B.V. All rights reserved.